PDB-9x3m: Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidas...

ID or keywords:

Entry

Database: PDB / ID: 9x3m

Title

Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.

Components

Xylan 1,4-beta-xylosidase

Keywords

HYDROLASE / beta-xylosidase / Xylose

Function / homology

Function and homology information

xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process / carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Pseudopedobacter saltans DSM 12145 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Vishwakarma, P. / Sachdeva, E. / Ethayathulla, A.S. / Goyal, A. / Singh, T.P. / Kaur, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.
Authors: Vishwakarma, P. / Sachdeva, E. / Ethayathulla, A.S. / Goyal, A. / Singh, T.P. / Kaur, P.

History

Deposition	Oct 9, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 7, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9x3m.cif.gz	691.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9x3m.ent.gz	549.4 KB	Display	PDB format
PDBx/mmJSON format	9x3m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9x3m_validation.pdf.gz	8.2 MB	Display	wwPDB validaton report
Full document	9x3m_full_validation.pdf.gz	8.2 MB	Display
Data in XML	9x3m_validation.xml.gz	140.5 KB	Display
Data in CIF	9x3m_validation.cif.gz	178 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x3/9x3m ftp://data.pdbj.org/pub/pdb/validation_reports/x3/9x3m	HTTPS FTP

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Related structure data

Related structure data	8hcjS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Xylan 1,4-beta-xylosidase

B: Xylan 1,4-beta-xylosidase

C: Xylan 1,4-beta-xylosidase

D: Xylan 1,4-beta-xylosidase

E: Xylan 1,4-beta-xylosidase

F: Xylan 1,4-beta-xylosidase

G: Xylan 1,4-beta-xylosidase

H: Xylan 1,4-beta-xylosidase

hetero molecules

390 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Xylan 1,4-beta-xylosidase

B: Xylan 1,4-beta-xylosidase

C: Xylan 1,4-beta-xylosidase

D: Xylan 1,4-beta-xylosidase

hetero molecules

defined by author
Evidence: gel filtration, The gel filtration chromatogram revealed the protein eluted as a tetramer
195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Xylan 1,4-beta-xylosidase

F: Xylan 1,4-beta-xylosidase

hetero molecules

G: Xylan 1,4-beta-xylosidase

H: Xylan 1,4-beta-xylosidase

hetero molecules

defined by author
195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.585, 89.435, 138.443
Angle α, β, γ (deg.)	102.818, 94.019, 97.882
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 22 - 453 / Label seq-ID: 1 - 432

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Xylan 1,4-beta-xylosidase Mass: 48510.477 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudopedobacter saltans DSM 12145 (bacteria) Strain: ATCC 51119/DSM 1 / Gene: Pedsa_2569 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0S5E9, xylan 1,4-beta-xylosidase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar	ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM) Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₅H₁₀O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 5% propanol, 0.1M imidazole and 14% PEG 3550.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 29, 2023
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 2.8→47.842 Å / Num. obs: 78398 / % possible obs: 93 % / Redundancy: 1.8 % / B_iso Wilson estimate: 21.44 Å² / CC_1/2: 0.9 / R_merge(I) obs: 0.17 / R_rim(I) all: 0.24 / Net I/av σ(I): 4 / Net I/σ(I): 4
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / Num. unique obs: 73759 / CC_1/2: 0.72 / R_rim(I) all: 0.52 / R_sym value: 0.37 / % possible all: 94

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8HCJ

8hcj

Resolution: 2.8→47.841 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.839 / WR_factor R_free: 0.283 / WR_factor R_work: 0.229 / SU B: 21.975 / SU ML: 0.408 / Average fsc free: 0.9496 / Average fsc work: 0.9677 / Cross valid method: FREE R-VALUE / ESU R Free: 0.488 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2728	3966	5.103 %
R_work	0.2183	73759	-
all	0.221	-	-
obs	-	77725	93.048 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.778 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9 Å²	-0.01 Å²	2.517 Å²
2-	-	-1.118 Å²	0.451 Å²
3-	-	-	-0.444 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.841 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27396	0	96	244	27736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	28299
X-RAY DIFFRACTION	r_angle_refined_deg	2.317	1.797	38422
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.852	5	3450
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.352	5	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.128	10	4496
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.996	10	1312
X-RAY DIFFRACTION	r_chiral_restr	0.149	0.2	3945
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	22500
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	10973
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	19133
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	801
X-RAY DIFFRACTION	r_metal_ion_refined	0.192	0.2	37
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.112	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.351	2.296	13818
X-RAY DIFFRACTION	r_mcangle_it	3.791	4.128	17259
X-RAY DIFFRACTION	r_scbond_it	3.303	2.427	14481
X-RAY DIFFRACTION	r_scangle_it	4.99	4.375	21162
X-RAY DIFFRACTION	r_lrange_it	6.638	23.659	40555
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.103	0.05	13662
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.097	0.05	13764
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.097	0.05	13779
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.099	0.05	13734
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.097	0.05	13734
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.098	0.05	13679
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.097	0.05	13776
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.101	0.05	13714
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.099	0.05	13749
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.097	0.05	13732
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.098	0.05	13593
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.095	0.05	13713
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.099	0.05	13753
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.095	0.05	13909
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.094	0.05	13838
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.091	0.05	13794
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.099	0.05	13696
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.09	0.05	13871
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.089	0.05	13919
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.093	0.05	13750
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.091	0.05	13811
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.089	0.05	13895
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.095	0.05	13661
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.096	0.05	13710
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.086	0.05	13896
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.099	0.05	13578
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.094	0.05	13797
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.098	0.05	13713

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10337	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10337	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09691	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09691	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09695	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09695	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09867	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.09867	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09714	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.09714	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09737	0.05009
7	14	H	X-RAY DIFFRACTION	Local ncs	0.09737	0.05009
8	15	B	X-RAY DIFFRACTION	Local ncs	0.10099	0.05009
8	16	C	X-RAY DIFFRACTION	Local ncs	0.10099	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.09872	0.05009
9	18	D	X-RAY DIFFRACTION	Local ncs	0.09872	0.05009
10	19	B	X-RAY DIFFRACTION	Local ncs	0.097	0.05009
10	20	E	X-RAY DIFFRACTION	Local ncs	0.097	0.05009
11	21	B	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
11	22	F	X-RAY DIFFRACTION	Local ncs	0.09816	0.05009
12	23	B	X-RAY DIFFRACTION	Local ncs	0.09546	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.09546	0.05009
13	25	B	X-RAY DIFFRACTION	Local ncs	0.0992	0.05009
13	26	H	X-RAY DIFFRACTION	Local ncs	0.0992	0.05009
14	27	C	X-RAY DIFFRACTION	Local ncs	0.0952	0.05009
14	28	D	X-RAY DIFFRACTION	Local ncs	0.0952	0.05009
15	29	C	X-RAY DIFFRACTION	Local ncs	0.09431	0.05009
15	30	E	X-RAY DIFFRACTION	Local ncs	0.09431	0.05009
16	31	C	X-RAY DIFFRACTION	Local ncs	0.09072	0.05009
16	32	F	X-RAY DIFFRACTION	Local ncs	0.09072	0.05009
17	33	C	X-RAY DIFFRACTION	Local ncs	0.09922	0.05009
17	34	G	X-RAY DIFFRACTION	Local ncs	0.09922	0.05009
18	35	C	X-RAY DIFFRACTION	Local ncs	0.08987	0.05009
18	36	H	X-RAY DIFFRACTION	Local ncs	0.08987	0.05009
19	37	D	X-RAY DIFFRACTION	Local ncs	0.08893	0.05009
19	38	E	X-RAY DIFFRACTION	Local ncs	0.08893	0.05009
20	39	D	X-RAY DIFFRACTION	Local ncs	0.09329	0.05009
20	40	F	X-RAY DIFFRACTION	Local ncs	0.09329	0.05009
21	41	D	X-RAY DIFFRACTION	Local ncs	0.09143	0.05009
21	42	G	X-RAY DIFFRACTION	Local ncs	0.09143	0.05009
22	43	D	X-RAY DIFFRACTION	Local ncs	0.08905	0.05009
22	44	H	X-RAY DIFFRACTION	Local ncs	0.08905	0.05009
23	45	E	X-RAY DIFFRACTION	Local ncs	0.09504	0.05009
23	46	F	X-RAY DIFFRACTION	Local ncs	0.09504	0.05009
24	47	E	X-RAY DIFFRACTION	Local ncs	0.09591	0.05009
24	48	G	X-RAY DIFFRACTION	Local ncs	0.09591	0.05009
25	49	E	X-RAY DIFFRACTION	Local ncs	0.08576	0.05009
25	50	H	X-RAY DIFFRACTION	Local ncs	0.08576	0.05009
26	51	F	X-RAY DIFFRACTION	Local ncs	0.09856	0.05009
26	52	G	X-RAY DIFFRACTION	Local ncs	0.09856	0.05009
27	53	F	X-RAY DIFFRACTION	Local ncs	0.09416	0.05009
27	54	H	X-RAY DIFFRACTION	Local ncs	0.09416	0.05009
28	55	G	X-RAY DIFFRACTION	Local ncs	0.09815	0.05009
28	56	H	X-RAY DIFFRACTION	Local ncs	0.09815	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.8-2.873	0.377	330	0.322	5523	0.325	6224	0.908	0.936	94.0392	0.33
2.873-2.951	0.577	247	0.541	4744	0.543	5980	0.898	0.912	83.4615	0.695
2.951-3.036	0.407	289	0.348	5198	0.352	5806	0.93	0.949	94.5057	0.358
3.036-3.129	0.323	297	0.248	5043	0.253	5658	0.935	0.963	94.3796	0.258
3.129-3.231	0.291	249	0.221	4979	0.225	5542	0.95	0.968	94.3342	0.226
3.231-3.344	0.278	248	0.22	4771	0.223	5332	0.952	0.971	94.1298	0.226
3.344-3.47	0.279	235	0.22	4555	0.223	5104	0.954	0.973	93.848	0.225
3.47-3.611	0.277	239	0.213	4390	0.216	4936	0.957	0.978	93.7804	0.215
3.611-3.77	0.282	208	0.236	4197	0.238	4741	0.942	0.965	92.9129	0.236
3.77-3.953	0.263	218	0.2	3974	0.203	4530	0.959	0.978	92.5386	0.204
3.953-4.165	0.235	212	0.17	3809	0.173	4307	0.969	0.984	93.3596	0.176
4.165-4.416	0.231	183	0.164	3604	0.167	4075	0.962	0.985	92.9325	0.172
4.416-4.718	0.174	184	0.143	3374	0.145	3842	0.982	0.987	92.608	0.154
4.718-5.092	0.186	151	0.134	3110	0.136	3548	0.98	0.989	91.9109	0.142
5.092-5.572	0.196	174	0.155	2972	0.158	3317	0.981	0.988	94.8447	0.162
5.572-6.219	0.22	167	0.19	2684	0.192	2968	0.974	0.984	96.058	0.196
6.219-7.161	0.23	119	0.184	2384	0.186	2615	0.974	0.984	95.717	0.191
7.161-8.721	0.23	100	0.177	2042	0.179	2247	0.973	0.984	95.3271	0.188
8.721-12.134	0.217	82	0.18	1537	0.181	1735	0.961	0.982	93.3141	0.196
12.134-47.841	0.313	34	0.311	869	0.311	1010	0.955	0.95	89.4059	0.355

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